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- PDB-6uj0: Unbound BACE2 mutant structure -

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Basic information

Entry
Database: PDB / ID: 6uj0
TitleUnbound BACE2 mutant structure
Components
  • Beta-secretase 2
  • unidentified polypeptide
KeywordsPEPTIDE BINDING PROTEIN / aspartic protease
Function / homology
Function and homology information


memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / Golgi apparatus / endoplasmic reticulum / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE2 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsYen, Y.C. / Ghosh, A.K. / Mesecar, A.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS) United States
CitationJournal: Acs Chem Neurosci / Year: 2021
Title: A Structure-Based Discovery Platform for BACE2 and the Development of Selective BACE Inhibitors.
Authors: Yen, Y.C. / Kammeyer, A.M. / Tirlangi, J. / Ghosh, A.K. / Mesecar, A.D.
History
DepositionOct 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-secretase 2
B: Beta-secretase 2
C: unidentified polypeptide
D: unidentified polypeptide


Theoretical massNumber of molelcules
Total (without water)100,1114
Polymers100,1114
Non-polymers00
Water3,099172
1
A: Beta-secretase 2
C: unidentified polypeptide


Theoretical massNumber of molelcules
Total (without water)50,0562
Polymers50,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-3 kcal/mol
Surface area15900 Å2
MethodPISA
2
B: Beta-secretase 2
D: unidentified polypeptide


Theoretical massNumber of molelcules
Total (without water)50,0562
Polymers50,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-2 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.603, 58.982, 84.555
Angle α, β, γ (deg.)113.394, 93.673, 96.382
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Beta-secretase 2 / / Aspartic-like protease 56 kDa / Aspartyl protease 1 / Asp 1 / Beta-site amyloid precursor protein ...Aspartic-like protease 56 kDa / Aspartyl protease 1 / Asp 1 / Beta-site amyloid precursor protein cleaving enzyme 2 / Beta-site APP cleaving enzyme 2 / Down region aspartic protease / DRAP / Memapsin-1 / Membrane-associated aspartic protease 1 / Theta-secretase


Mass: 49441.996 Da / Num. of mol.: 2 / Mutation: E269A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE2, AEPLC, ALP56, ASP21, CDA13, UNQ418/PRO852 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9Y5Z0, memapsin 1
#2: Protein/peptide unidentified polypeptide


Mass: 613.749 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, pH = 6 1.26 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 43513 / % possible obs: 97 % / Redundancy: 2.2 % / Biso Wilson estimate: 34.23 Å2 / Rpim(I) all: 0.069 / Net I/σ(I): 17.7
Reflection shellResolution: 2.15→2.2 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4122 / Rpim(I) all: 0.372

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EWY

2ewy


Resolution: 2.15→28.04 Å / SU ML: 0.2628 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.4932
RfactorNum. reflection% reflection
Rfree0.2578 2198 5.06 %
Rwork0.2198 --
obs0.2218 43480 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5746 0 0 172 5918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085884
X-RAY DIFFRACTIONf_angle_d0.84628001
X-RAY DIFFRACTIONf_chiral_restr0.0642896
X-RAY DIFFRACTIONf_plane_restr0.00461019
X-RAY DIFFRACTIONf_dihedral_angle_d15.68742085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.190.38011150.30892321X-RAY DIFFRACTION87.34
2.19-2.240.3721450.29912589X-RAY DIFFRACTION97.12
2.24-2.30.3781450.29862544X-RAY DIFFRACTION95.76
2.3-2.360.31011400.28032588X-RAY DIFFRACTION97.57
2.36-2.430.32511410.26992581X-RAY DIFFRACTION97.35
2.43-2.50.34591400.27092582X-RAY DIFFRACTION97.6
2.5-2.590.31331450.25672627X-RAY DIFFRACTION97.71
2.59-2.70.34041120.24562620X-RAY DIFFRACTION97.89
2.7-2.820.28571550.23782612X-RAY DIFFRACTION98.02
2.82-2.970.2681290.23322589X-RAY DIFFRACTION97.98
2.97-3.160.28541130.23162643X-RAY DIFFRACTION97.97
3.16-3.40.26881400.22162612X-RAY DIFFRACTION98.29
3.4-3.740.24781130.20142629X-RAY DIFFRACTION97.93
3.74-4.280.20911660.18592589X-RAY DIFFRACTION98.08
4.28-5.390.18331420.17312618X-RAY DIFFRACTION98.68
5.39-28.040.2381570.20512538X-RAY DIFFRACTION95.98

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